About eAED

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About eAED

Quanwei Zhang
Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1? 

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei

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Re: About eAED

Xabier Vázquez Campos

On 5 October 2017 at 09:31, Quanwei Zhang <[hidden email]> wrote:
Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1? 

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei

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Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA

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Re: About eAED

Carson Holt-2
In reply to this post by Quanwei Zhang
eAED is an extended AED calculation that does some inference about the evidence (i.e. checks reading frame and not just overlap, and may infer support for an exon if by splice sites are confirmed etc.). If eAED is 1 that means that while there is evidence supporting the model, the evidence is more likely to be spurious, so it may be a false model.

—Carson

 

> On Oct 4, 2017, at 4:31 PM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1.
>
> Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1?  
>
> >maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35
>
> Thanks
>
> Best
> Quanwei
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: About eAED

Carson Holt-2
In reply to this post by Xabier Vázquez Campos
This one is an even better explanation than the answer I just gave. Thank you.

—Carson

On Oct 4, 2017, at 4:35 PM, Xabier Vázquez-Campos <[hidden email]> wrote:


On 5 October 2017 at 09:31, Quanwei Zhang <[hidden email]> wrote:
Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1? 

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei

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--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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Re: About eAED

Quanwei Zhang
Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?

The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED?

Best
Quanwei

 

2017-10-04 18:39 GMT-04:00 Carson Holt <[hidden email]>:
This one is an even better explanation than the answer I just gave. Thank you.

—Carson

On Oct 4, 2017, at 4:35 PM, Xabier Vázquez-Campos <[hidden email]> wrote:


On 5 October 2017 at 09:31, Quanwei Zhang <[hidden email]> wrote:
Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1? 

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei

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maker-devel mailing list
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--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



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Re: About eAED

Carson Holt-2
The previous linked comment explains in detail —> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ

Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).

—Carson


On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <[hidden email]> wrote:

Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?

The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED?

Best
Quanwei

 

2017-10-04 18:39 GMT-04:00 Carson Holt <[hidden email]>:
This one is an even better explanation than the answer I just gave. Thank you.

—Carson

On Oct 4, 2017, at 4:35 PM, Xabier Vázquez-Campos <[hidden email]> wrote:


On 5 October 2017 at 09:31, Quanwei Zhang <[hidden email]> wrote:
Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1? 

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei

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maker-devel mailing list
[hidden email]
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--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




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Re: About eAED

Carson Holt-2
eAED can be better for edge cases, but neither is perfect. Low AED generally correlates with better models. But a high AED does not mean the model doesn’t exist, it just means you should spend a little more time deciding if you really believe it or not.

—Carson


On Oct 4, 2017, at 8:38 PM, Carson Holt <[hidden email]> wrote:

The previous linked comment explains in detail —> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ

Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).

—Carson


On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <[hidden email]> wrote:

Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?

The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED?

Best
Quanwei

 

2017-10-04 18:39 GMT-04:00 Carson Holt <[hidden email]>:
This one is an even better explanation than the answer I just gave. Thank you.

—Carson

On Oct 4, 2017, at 4:35 PM, Xabier Vázquez-Campos <[hidden email]> wrote:


On 5 October 2017 at 09:31, Quanwei Zhang <[hidden email]> wrote:
Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1? 

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





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Re: About eAED

Quanwei Zhang
Thanks for your explanation.

Best
Quanwei

2017-10-04 22:43 GMT-04:00 Carson Holt <[hidden email]>:
eAED can be better for edge cases, but neither is perfect. Low AED generally correlates with better models. But a high AED does not mean the model doesn’t exist, it just means you should spend a little more time deciding if you really believe it or not.

—Carson



On Oct 4, 2017, at 8:38 PM, Carson Holt <[hidden email]> wrote:

The previous linked comment explains in detail —> https://groups.google.com/forum/#!msg/maker-devel/wtmNRtRa-ko/iC4KTuIitGEJ

Basically the middle support of exon is inferred from edge support even though no overlap exists (so eAED infers support and AED does not).

—Carson


On Oct 4, 2017, at 8:35 PM, Quanwei Zhang <[hidden email]> wrote:

Thank you all.  Most time, the AED is equal to or lower than eAED, but there are some genes whose eAED is smaller than AED. I feel the eAED is more stringent than AED. Would you give me an example, under what condition eAED can be smaller than AED?

The default maker2 gene set includes all genes with AED less than 1.  Do you think eAED is a better choice to filter gene models than AED?

Best
Quanwei

 

2017-10-04 18:39 GMT-04:00 Carson Holt <[hidden email]>:
This one is an even better explanation than the answer I just gave. Thank you.

—Carson

On Oct 4, 2017, at 4:35 PM, Xabier Vázquez-Campos <[hidden email]> wrote:


On 5 October 2017 at 09:31, Quanwei Zhang <[hidden email]> wrote:
Hello:

I ran the maker2 pipeline and got the default gene sets (with AED<1). But I found there are several hundred genes with eAED 1.

Below is an example, the gene has AED 0.05 and eAED 1. I wonder what can be the reason of the great difference between AED and eAED. For this gene it has a very low AED score, is it still a reliable gene model if its eAED equals 1? 

>maker-Contig2656-snap-gene-269.6-mRNA-1 protein AED:0.05 eAED:1.00 QI:75|0|0|1|0|0|2|111|35

Thanks

Best
Quanwei

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org






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